registration | conditions

SEQtools downloads
setup files	SEQtools.exe	6.802 mb
update	SEQupdate.exe	1.685 mb
auxiliary programs 19.11.2002	auxiliary8.exe	6.280 mb
manual, self-extracting pdf	SEQmanual.exe	3.363 mb
sample sequences	SEQsamples.exe	0.283 mb

version information...		* when the version number of   the setup is smaller than the   version number of the update you   need to update after the setup to   get the latest version of SEQtools
setup*    update     auxiliary	8.0.713 8.0.720 20.10.2002

 

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install SEQtools for the first time

The self-extracting installation file for SEQtools contains all files necessary to install the basic SEQtools application. After downloading unpack the file to extract the setup files. Then run setup.exe to install SEQtools on your PC.  If you wish to include functions depending on NCBI support and trace file processing and viewing, you must also download the self-extracting auxiliary8.exe file and install the programs as described below. SEQtools communicates directly with two independent applications, GeneDoc for editing and annotating multi-sequence alignments and TreeView for building phylogenetic trees. In both cases install the programs on your PC. Then use general preferences in SEQtools to create links between SEQtools and the two programs by including them in the SEQtools launch menu. When you install SEQtools for the first time you automatically get a demo license which is valid for four months. When this expires you can extend the demo license by getting an extended demo license which is also free of charge and covers the next four months. You can continue renewing your extended demo license for as long as you wish without having to pay anything. You can also pay US$ 30 to get a full license which covers the next 100 years (which should be sufficient for most of us...) and which allows you to upgrade as often as you wish. You can read more about about registration, licenses and prices on the registration page.

update an existing installation

The self-extracting SEQupdate.exe update file contains the latest versions of SEQtools.exe, SEQtools.hlp, SEQtools.cnt and gcg_uniq.dat for updating an existing installation of SEQtools. SEQtools looks for new updates each time you start the program. If an update is available you will be informed and SEQtools will offer to download and install the update. If this fail you can download the update files yourself an replace the existing files with the new ones. WARNING Replacing your current version of SEQtools with an update not covered by your license will cause SEQtools to stop working. In this event, just use the registration form to get a new registration key allowing you to use the update.  Or buy a full license which includes unlimited updating.

sample sequence files

Sample sequences: To give you an impression of how SEQtools handles nucleotide and protein sequences, I have included two annotated multi-sequence files, dna.fms and protein.fms, in the self-extracting SEQsamples.exe file. To use the sample files, decompress the SEQsamples.exe to: c:\~seqtools\samples\. Then copy the dnaDB database files to the main SEQtools folder. Start SEQtools, click File/Load Sequence Files/Nucleotide or Amino Acid Sequences, click Done when the project form appears and navigate to c:\~seqtools\samples\dna.fms or protein.fms, click Add To List and finally Load Files. (the sample files are not yet available but will appear soon, 05.01.2002)

auxiliary programs - update: 19.11.2002

After installing SEQtools start the program and click Help/SEQtools Configuration... to display the the current configuration of SEQtools. Then simply click Fetch Auxiliary Programs to start downloading and installing the auxiliary programs. When downloading is complete, close and restart SEQtools to implement the the auxiliary programs. If this fails, it is possible to carry out the installation of auxiliary programs manually: Install and run SEQtools (to create the default SEQtools dos folder, ST8_TEMP, located in the windows folder of your pc). Download the auxiliary8.exe file directly from the SEQtools download page. After downloading run the self-extracting auxiliary8.exe. By default the self extractor suggests to place the extracted files in "c:\~seqtools\auxiliary". Copy the update files to the SEQtools program folder. Each time SEQtools starts it scans the main program folder for updates, local databases etc. If you are behind a firewall read the information below about setting up your local server permissions to enable NCBI programs to communicate with the Blast and Entrez servers at NCBI. The auxiliary file includes...

clustal	required for multi-sequence alignment in SEQtools. Clustalx is a stand-alone program launched from SEQtools with the selected sequences as parameters. Clustalw is a command line DOS program entirely controlled by the SEQtools user interface. The clustalx/w exe files and the clustal help file must be present in the main SEQtools directory to allow SEQtools to activate the multi-sequence alignment function. Version 1.81 of clustalx/w is included in the auxiliary file available for downloading. The clustal programs were written by: Toby Gibson EMBL, Heidelberg, Germany. Des Higgins UCC, Cork, Ireland. Julie Thompson IGBMC, Strasbourg, France. Francois Jeanmougin IGBMC, Strasbourg, France.
blastall formatdb bl2seq blastclust	are all required to set up SEQtools for creating and searching local databases with the five blast programs and for comparing sequences. The exe-files as well as the files contained in the data directory are all included in the auxiliary file. Current version is 2.2.4
blastcl3	SEQtools uses this NCBI client for database searching on GenBank databases.  In some cases there may be a problem if you are behind a firewall. Consult the NCBI blastcl3 helpfile and/or your system administrator for advice.
entrez	is used to retrieve sequence records and Medline entries from Entrez
convert_trace	enables SEQtools to extract and import chromatograms generated by the most common auto-sequencers. In addition to convert_trace, the two dll's: read and zlib are required.
chromas	is used to view chromatogram files. Note that versions of chromas earlier than 162 are freeware whilst newer versions require registration and a license fee. Read more about chromas on the chromas website.

GeneDoc

Download GeneDoc from the GeneDoc homepage To enable data transfer between SEQtools and GeneDoc, install GeneDoc from the its setup file. Then, in SEQtools use the Launch option in general preferences to include genedoc.exe in the launch menu.

TreeView

Download  TreeView from the original TreeView homepage To enable data transfer between SEQtools and TreeView, install Treeview from the its setup file. Then, in SEQtools use the Launch option in general preferences to include treeview.exe in the launch menu.

Chromas

Download Chromas 213 (licensed), Chromas 145 (free) or visit the original Chromas homepage Chromas is included in the auxiliary8.exe file and the data transfer between SEQtools and Chromas is automatically established when the auxiliary programs are installed.

ReBase

Go to the ReBase homepage Updated restriction enzyme data files can be downloaded from ReBase. In addition to enzyme data files, ReBase contains a very useful search function which allows you to search their data base with the name of an enzyme or with a recognition pattern. Download the restriction enzyme data file in GCG format.  How to convert GCG enzyme files to SEQtools format... SEQtools uses a slightly different enzyme data file format so it is necessary to use the Convert GCG Data Files function under the Utilities menu to change the format so that the data file can be used with SEQtools.

system requirements

SEQtools only runs on 32bit Windows based PC's *) and it is not possible to run the program on Macs, Unix and other non-Windows computers. Also remember that SEQtools is NOT intended for very large projects - or for very long sequences. In such cases you need to use more sophisticated and powerful software solutions. Obviously the program runs more efficiently the more powerful the computer is. A Pentium 266 Mhz with 64 Mb RAM works well for small projects, i.e., 1-500 sequences each of 500 bp. If you intend to work with larger projects, it is a good idea to add more RAM to your PC. Currently we are using a dual processor 1.8 Ghz Pentium IV equipped with 1 Gb RAM. The current version of SEQtools is unable load sequence files unless they are located on the same PC as the program itself - or you have assigned a drive letter to the folder on a remote drive. If for some reason, the remote folder is not available (for example because the remote PC is turned off) you will not be notified by SEQtools. As the entire program is written by a single person, testing the program on the numerous PC's and printers available is not possible. Printing is especially difficult to handle. Printing has been tested with HP LaserJet 4L, 6P and HP930C but probably also works with other printers.  If you have problems running SEQtools on your PC, please let me try to help you. Write an e-mail with as many details as possible describing the nature of the problem. *) According to some users SEQtools runs fine under Virtual PC on the Macintosh.

Firewalls

Firewalls installed on local servers may in some cases prevent SEQtools from communicating with external resources such as the NCBI blast server and the auto-retrieval function of SEQtools used to install auxiliary programs (various NCBI programs, Clustal etc.).  While I will try to assist you as much as I can, it often turns out that such problems are very difficult to solve. The NCBI blastcl3 helpfile may be helpful in setting up the communication between SEQtools and NCBI programs through a firewall.

 

 

 

 

 

 

 

 

 

   

Page updated 06-03-03  by  S.W. Rasmussen